Gene Expression & Genotyping

Services & Fees
GENE EXPRESSION & GENOTYPING:    Home  |  Staff & Contact  |  ServicesInstruments  |  Getting Started  |  Sample Requirements |  Core Resources

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Offered Services

Antibody Sequencing

The service includes cloning and sequencing mouse heavy and light chains starting with total RNA, alignments of the heavy and light chains, to a detailed project report with annotated antibody DNA, protein sequences and CDRs.

Bravo Automations

Bravo 16s and RNAseq Library Automation (Bravo Automations) 

16s ribosomal RNA sequencing can be used to identify and compare bacteria present within a given sample.

RNA-Seq is a powerful research tool for expression and variant analysis. Its’ application includes quantifying mRNA abundance; determining the transcriptional structure of genes: start sites, 5′ and 3′ ends, and splicing patterns; comparably detecting the changing expression levels of each transcript during development and under different conditions. It picks up all sequences that are present in the cell, regardless of their annotation status.

Gene Expression Core offers library preparation automation by Agilent Bravo Automation Workstation.The constructed libraries can be run on all NextGen sequencing platforms: Illumina HiSeq, MiSeq, and NextSeq.  Sequence can be done by ICBR NextGen Sequencing Core.

We also offer Agilent’s SureSelect Target Enrichment platform which allows you to focus your NextGen sequencing workflow on key genomic regions of interest while reducing cost per sample. Other NextGen relative services include cDNA library construction, normalization and rRNA depletion (Ribominus). If requested, we will directly deliver the libraries to our ICBR NextGen Sequencing Core with an e-mail notification to you.  Otherwise the library will be returned to you.

Custom Bravo Run (Bravo Automations) 

The service includes the Bravo consumables and run assistance.

Cell-Line Authentication (Human)

This assay works only with human cell-lines. Submit 5×10^6 cells in 100ul 1X PBS on ice. Cells can be submitted fresh or frozen. If submitting frozen samples, they must have been snap frozen. Cell-line will be authenticated using GenePrint 10 System from Promega. The GenePrint 10 System allows co-amplification of repeat regions of nine short tandem repeat human loci, including the ASN-0002 loci (TH01, TPOX, vWA, Amelogenin, CSF1PO, D16S539, D7S820, D13S317 and D5S818) as well as D21S11. Data will be analyzed using GeneMapper v4.0 software and a Genotype report of your sample with number of repeats for each marker listed will be generated.

*The assay will not detect very low level of contaminants.

Custom Project

For NEW customers and NEW projects: Schedule a consultation to discuss experimental design and prepare a project outline with an ICBR staff member.

Digital PCR Analysis

This service allows the customer to do absolute quantification, rare allele detection, quantification using TaqMan SNP array and CNV (Copy Number Variation) in a more sensitive, specific, and precise way.

Genotyping

Fragment Analysis (Genotyping) 

Genotypic characterization using the AB3730 (96 capillary technology).

There are 3 different dye settings availble 1) 6-FAM, VIC, NED and PET; 2) 5-FAM, JOE and NED; 3) 6-FAM, HEX and NED.

Other Genotyping Services (Genotyping)
A variety of genotypic characterization services are offered.  Customers can request primer design, microsatellite sample preparation, AFLP PCR, genotyping by qPCR, large-scale mouse genotyping with mouse tails or ear punches.  Customers can also provide ready-to-run samples as dye-labeled pools for analysis on select instruments.

STR Analysis (Genotyping) 

1. STR analysis using the PowerPlex® 16 HS System from Promega.
2. The PowerPlex® 16 HS System allows co-amplification and three-color detection of sixteen loci (fifteen STR loci and Amelogenin), including Penta E, D18S51, D21S11, TH01, D3S1358, FGA, TPOX, D8S1179,vWA, Amelogenin, Penta D, CSF1PO, D16S539, D7S820, D13S317 and D5S818.
3. The samples will be processed on ABI 3730 Genome Analyzer.
4. Data will be analyzed using GeneMapper® v4.0 software.
5. Positive and negative controls will be run.

Microarray

Affymetrix Chip Hybridization and Scan (Microarray) 

Customer provides labeled cRNA or ssDNA.  Service includes hybridization, wash and scan of chip, and delivery of raw data.

Affymetrix Full Service (Microarray) 

Microarrays are hybridization-based procedures that measure genomic-wide gene expression in one signal experiment. The 3’ IVT Expression Analysis uses RNA to produce cDNA from reverse transcription, and then generate multiple copies of biotin-labeled aRNA. This labeled aRNA is used for hybridization to GeneChip expression arrays.

The GeneChip® Gene 1.0 ST Array System offers the most advanced and cost-effective gene expression profiling option for whole transcript coverage. Available organisms of GeneST and Exon arrays are human, rat and mouse. We are using the Whole Transcript (WT) Assay approach the GeneST and Exon Array System.

We also can process Affymetrix samples using NuGen kit for low amount or degraded RNA samples.

Data is returned in the form of CEL image files of the scan and a text file of Array Metric QC.

RNA DNA QC

Agilent 2100 Bioanalyzer/2200 TapeStation Analysis (RNA DNA QC)

**Attention: If you are submitting libaries for a sequencing run in the NextGen core, please request their library evaluation services**

The Agilent 2100 Bioanalyzer and 2200 TapeStation system automatically perform the multiple steps of gel-based electrophoresis, replacing the need to run agarose gels to separate and quantitate your RNA or DNA samples.  A software tool, RNA Integrity Number (RIN) can help scientists estimate the integrity of total RNA samples.  Data is returned in the form of PDF.

Sample Concentration Measurement (RNA DNA QC)

Quantitate micro-volume of samples via NanoDrop, or Qubit. Please provide the DNA size if caculated nM concentration is needed.

RNA-Seq and NextGen Library Related Service

RNA-Seq is a powerful research tool for expression and variant analysis. Its’ application includes quantifying mRNA abundance; determining the transcriptional structure of genes; start sits, 5′ and 3′ ends, and splicing patterns; comparably detecting the changing expression levels of each transcript during development and under different conditions. It picks up all sequences that are present in the cell, regardless of their annotation status.

Sample Preparation

Service includes gDNA/RNA extraction, RNA clean up, PCR purification, revers transcription, ds cDNA synthesis, TA cloning and more

Sequencing Load Only

Five different load only services are offered. They are 1) Edited Load only: 700-1100 bases; 2) Edited Load only: Up to 600 bases; 3) Un-edited Load Only; 4) MLPA Load Only: Marker pre-added; and 5) MLPA Load Only: Marker to be added. For MLPA Load Only services, electrophoresis, fragment analysis and raw data delivery are included.

Single Cell Analysis (10X Genomics Chromium)

The 10x Genomics Chromium Controller System

The 10X Genomics Chromium Controller instrument is designed to capture thousands of single cells or DNA fragment, and combined them with reagents and gel bead (which contains barcoded oligonucleotides) in emulsion droplets (GEMs) to perform a variety of assays. Each GEM are uniquely barcoded.

It can perform Single Cell RNA-seq, Single Cell Copy Number Variation Profiling, Single Cell Immune Repertoire Profiling, Single Nuclei Expression Profiling, and Single Cell CITE-seq. For those assays, it can capture 500-10,000 individual cells per sample. Additionally, it partitions high molecular weight (HMW) DNA into individual GEMs to capture long-range information using Illumina sequencer. This assay requires low input of high molecular weight DNA to produce “linked read” information, which can be used for assembling genomes, assessing structural variants and obtaining genome phase information.

qPCR

General Service (qPCR)

qPCR analysis offered at Gene Expression and Genotyping are: SYBR® or TaqMan™ reagents allowing absolute, relative, relative standard or comparative Ct quantification. Services includes but not limited to qPCR Absolute Quantification Data Analysis/Per Standard Curve; RT Profiler PCR arrays – chemistry; qPCR post amplification read (SNP); qPCR Mid service  on CFX (1 plate); qPCR Plate set-up for 384 well Absolute Quantitation; qPCR primer and probe sets assay design.

 
Quantification of NextGen Sequencing libraries by qPCR 

This method is widely used because its ability to target adapter sequences for a specific sequences in NextGen libraries. It enables accurate quantification of NextGen libraries. It measures the functional molecular of the libraries.
 
SYBR Green-based Detection (qPCR)

This real-time PCR assay uses SYBR Green Chemistry to detect PCR products as it accumulate during real time PCR process.

 
TaqMan-based Detection (qPCR)

This real-time PCR assay consists a target-specific probe and two gene specific primes that can increase the specificity of quantification PCR. The fluorescence single generated by probe allows quantitate measurements of the accumulated PCR product and increases the specificity of gene detection.

Service Price List

Last Updated: 08/2019

Affymetrix

Agilent

Antibody Sequencing

Bravo Automation

Cell-Line Authentication

CRISPR

Data Analysis

Digital PCR Analysis

General Services

Genotyping

RNA DNA QC

RNA DNA QC-Concentration Measurement

RNA-Seq & NextGen Related Services

Reagents & Supplies

Real-Time PCR

Sample Preparation

Sequencing Load Only

Shipping

Single Cell Analysis

qPCR